|Helen Kim, Ph.D.|
Joint appointment: Biochemistry and Molecular Genetics
Senior scientist, UAB Comprehensive Cancer Center
Senior scientist: UAB Center for Aging
Master of Forest Science, Yale University School of Forestry and Environmental Studies;
Ph.D., Biophysics, University of Virginia
Proteomics of dementia and age-related cognitive impairment: Our ultimate objective is to "discover" the protein differences that are different in demented brain (such as human Alzheimer's disease and mouse models of dementia) relative to healthy controls, and use this information to identify structure-function relationships for specific proteins that have relevance to human dementias. To do this, we utilize proteomics approaches, involving 2D gel electrophoresis of brain proteins, followed by mass spectrometry to identify and characterize the proteins/protein modifications determined to be significantly different between disease and control samples. This approach allows analysis of global protein differences between complex biological samples, without having a prior knowledge of what these differences might be.
Grape seed actions in the brain: The initial proteomics efforts that we published (Deshane et al., J. Agric. Food Chem, 2004) dealt with a major experimental approach in our lab, studying the effects of dietary supplements such as grape seed extract enriched in anti-oxidants for neuroprotective actions in mammalian brain. To do this, we compared 2D gel patterns of protein expression between the brains of animals given control diet and the brains of those given diet supplemented with grape seed extract. We determined that specific proteins were different in abundance between the brains of rats given grape seed extract vs control diet; almost all these proteins had previously been implicated by others in Alzheimerís disease, or in mouse models of dementia; interestingly, the majority of the directions of changes induced by grape seed were opposite to the directions of changes for the affected proteins determined by others in either AD brain, or transgenic mouse models of dementia, suggesting that indeed the grape seed extract was exerting neuroprotective actions. This was the first identification of specific proteins affected by oral intake of a complex dietary supplement such as grape seed, and the first to show a link of such effects with disease.
Structural and functional consequences of oxidations of proteins: In addition to global proteomics, where all possible protein differences are detected between biological samples, we are mapping and characterizing oxidations of specific brain proteins, to determine which oxidations are relevant in disease, and which of these are affected/prevented by anti-oxidants. We do this by derivatizing protein mixtures with dinitrophenylhydraziune (DNPH), which reacts with protein carbonyls, the most common form of protein oxidation, and with the carbonyls introduced onto proteins by adducts formed by oxidized lipids such as 4-hydroxynonenal or 4HNE. The samples are then studied by 2D gel Western blots with antibodies that recognize DNP. This approach has indicated that selected brain proteins are lower in oxidation in mouse demented brains after grape seed (Kim et al., 2005). One of these, the brain isoform of creatine kinase (CK-BB) is being studied by Shannon Eliuk, a graduate student in the lab; she is studying the activity of the recombinant human CK-BB enzyme activity after in vitro oxidation with HNE; for structural analysis, she is using fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) in collaboration with Dr. Mathew Renfrow (Biochemistry and Molecular Genetics) to map multiple amino acid sites of oxidation. Initial analysis with quadrupole time of flight mass spectrometry (Qtof-MS) indicated that several residues in the catalytic site of the CK-BB homodimer were modified (Eliuk et al., 2006).
Director, 2D Proteomics: In addition to directing her lab research, Dr. Kim directs the 2D Proteomics component of the UAB Comprehensive Cancer Center Mass Spectrometry and Proteomics Shared Facility, as well as providing proteomics core support for four centers, the UAB Center for Nutrient-Gene Interactions, (Barnes, PI); the UAB Polycystic Kidney Disease Research Core (Guay-Woodford, PI), the UAB Skin Disease Research Core (Elmets, PI), and the Purdue/UAB Botanicals Center for Age-Related Diseases (Weaver, PI; [Purdue]). In this capacity, she collaborates with several investigators in biological systems outside of the nervous system (see publications).
Fukuchi KI, Tahara K, Kim HD, Maxwell JA, Lewis TL, Accavitti-Loper MA, Kim H, Ponnazhagan S, Lalonde R. Anti-Abeta single-chain antibody delivery via adeno-associated virus for treatment of Alzheimer's disease. Neurobiol Dis. 2006 Jun 9; [Epub ahead of print]
Fukuchi K, Accavitti-Loper MA, Kim HD, Tahara K, Cao Y, Lewis TL, Caughey RC, Kim H, Lalonde R. Amelioration of amyloid load by anti-Abeta single-chain antibody in Alzheimer mouse model. Biochem Biophys Res Commun. 2006 May 26;344(1):79-86.
Sarkar P, Sarkar S, Ramesh V, Hayes BE, Thomas RL, Wilson BL, Kim H, Barnes S, Kulkarni A, Pellis N, Ramesh GT.Proteomic analysis of mice hippocampus in simulated microgravity environment. J Proteome Res. 2006 Mar;5(3):548-53.
Kim H, Deshane J, Barnes S, Meleth S. Proteomics analysis of the actions of grape seed extract in rat brain: technological and biological implications for the study of the actions of psychoactive compounds. Life Sci. 2006 Mar 27;78(18):2060-5.
Hsu HC, Zhou T, Kim H, Barnes S, Yang P, Wu Q, Zhou J, Freeman BA, Luo M, Mountz JD. Production of a novel class of polyreactive pathogenic autoantibodies in BXD2 mice causes glomerulonephritis and arthritis. Arthritis Rheum. 2006 Jan;54(1):343-55.
Kim, H. New nutrition, proteomics, and how both can enhance studies in cancer prevention and therapy. J Nutr. 2005 Nov;135(11):2715-8.
Cao D, Fukuchi KI, Wan H, Kim H, Li L. Lack of LDL receptor aggravates learning deficits and amyloid deposits in Alzheimer transgenic mice. Neurobiol Aging. 2005 Oct 14; [Epub ahead of print]
Peng N, Clark JT, Prasain J, Kim H, White CR, Wyss JM. Antihypertensive and cognitive effects of grape polyphenols in estrogen-depleted, female, spontaneously hypertensive rats. Am J Physiol Regul Integr Comp Physiol. 2005 Sep;289(3):R771-5.
Meleth S, Deshane J, Kim H. The case for well-conducted experiments to validate statistical protocols for 2D gels: different pre-processing = different lists of significant proteins. BMC Biotechnol. 2005 Feb 11;5:7.
Deshane J, Chaves L, Sarikonda KV, Isbell S, Wilson L, Kirk M, Grubbs C, Barnes S, Meleth S, Kim H. Proteomics analysis of rat brain protein modulations by grape seed extract. J Agric Food Chem. 2004 Dec 29;52(26):7872-83.
Kim H, Hall P, Smith M, Kirk M, Prasain JK, Barnes S, Grubbs C. Chemoprevention by grape seed extract and genistein in carcinogen-induced mammary cancer in rats is diet dependent.
Kim HD, Kong FK, Cao Y, Lewis TL, Kim H, Tang DC, Fukuchi K. Immunization of Alzheimer model mice with adenovirus vectors encoding amyloid beta-protein and GM-CSF reduces amyloid load in the brain.
Huang CM, Elmets CA, van Kampen KR, Desilva TS, Barnes S, Kim H, Tang DC. Prospective highlights of functional skin proteomics. Mass Spectrom Rev. 2005 Sep-Oct;24(5):647-60. Review.
Venkatraman A, Landar A, Davis AJ, Chamlee L, Sanderson T, Kim H, Page G, Pompilius M, Ballinger S, Darley-Usmar V, Bailey SM. Modification of the mitochondrial proteome in response to the stress of ethanol-dependent hepatotoxicity. J Biol Chem. 2004 May 21;279(21):22092-101.
Barnes S, Kim H. Nutriproteomics: identifying the molecular targets of nutritive and non-nutritive components of the diet. J Biochem Mol Biol. 2004 Jan 31;37(1):59-74.
Kim H. Depletion of acetylated alpha- tubulin during microtubule purification from bovine brain gray and white matter regions. J. Neurosci. Res. 1991. 172-182.
To contact Dr. Kim: